title: GenPhyloData: realistic simulation of gene family evolution.
abstract: BACKGROUND
  PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.
  
  
  RESULTS
  Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
  
  
  CONCLUSIONS
  The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
authors.affiliation: Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.
authors.forename: Joel
authors.initials: J
authors.lastname: Sjöstrand
authors.forename: Lars
authors.initials: L
authors.lastname: Arvestad
authors.forename: Jens
authors.initials: J
authors.lastname: Lagergren
authors.forename: Bengt
authors.initials: B
authors.lastname: Sennblad
mesh_terms: D001683:Biological Clocks / Q000235:genetics; D003198:Computer Simulation; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics*; D018014:Gene Transfer Techniques; D006801:Humans; D008954:Models, Biological; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D013045:Species Specificity